In this study, we consider problematic issues associated with harmonization of pharmacopoeial approaches to the assessment of the main physicochemical indicators of immunobiological medicinal products in the context of formation of a regulatory system of the Euro-Asian Economic Union (EAEU) with the purpose of ensuring the independence of the pharmaceutical market of the Russian Federation. Among the selected quality indicators of human immunoglobulin preparations, which are used in national and international pharmacopoeial standards, were selected the following: “Protein”, “Electrophoretic homogeneity”, and “Molecular parameters”. “Thiomersal”, “Phenol”, and “Aluminum” were selected to assess the quality of vaccines and anatoxins. The harmonization of the above methodological approaches to the assessment of a particular indicator is hampered by the historically evolved differences in the requirements and recommendations of the State Pharmacopoeia of the Russian Federation and the European Pharmacopoeia, recognized as the basis for the development of harmonized requirements of the EAEU pharmacopoeia. These differences relate to methodologies, standards for a particular indicator, and approaches to their metrological support (use of appropriate reference materials). In the course of the study, a comparative analysis of these differences was carried out. The tendency of most manufacturers to switch to the use of high-tech laboratory equipment based on high-performance liquid and/or gas chromatography and atomic absorption spectrometry is noted. Information on the development of these methods and the availability of appropriate reference materials is provided. The conducted comparative analysis indicates the relevance of the development and certification of pharmacopoeial reference materials for harmonized methods of determination of protein, electrophoretic homogeneity, and molecular parameters. Approaches to extending the application range of available pharmacopoeial reference materials are shown, taking into account the potential of improved methods of quality control of vaccines and anatoxins by quantitative content of preservatives and adjuvants. The Russian laboratory pharmaceutical practice is focused on the specifics of immunobiological preparations and the use of pharmacopoeial reference materials that enable intra- and inter-laboratory quality testing.